[Owl-devel] Residue contact potential

Dan Bolser dan.bolser at gmail.com
Fri Apr 9 10:31:19 EDT 2010

Hi AJ,

I hope your PhD is going well! I bet Cambridge is nice at the moment;
are the magnolia trees out yet?

I'm glad that the paper was of interest to you.

To compile the data for the analysis I did, I used the tools and
databases developed by colleagues while I was in the Structural
Proteomics group in the Otto-Warburg-Laboratory at the Max Planck
Institute for Molecular Genetics. The good news is that the group has
decided to make those tools publicly available via an open source
project at Bioinformatics.Org:


I have CC'ed this reply the open source mailing list for that group,
where you can ask any questions about what you will need to get up and
running. I have included my processing pipeline notes, and some basic
scripts for your reference (see 'sample_files.tar.gz').

JOSE: my python scripts say "from pypdb import Pdb"?

Unfortunately it is often very hard to find simple software
encapsulations of empirical potentials for protein scoring. This was
the reason why I couldn't rigorously compare the potentials I
developed to others in the literature.

GREAT NEWS! I was just collecting the set of files for you to look at
when I discovered I *have* created a 'stand alone' Perl program for
calculating scores! (Terrible memory!)

See the attached 'score_any_structure-2010.04.09.tar.gz'

Let me know how you get on.

All the best,

P.S. Will you ask Madan when he will get NCI back up? It's been down for years!


On 9 April 2010 14:26, A.J.Venkatakrishnan
<venkatakrishnan.a.j at gmail.com> wrote:
> Dear Dan,
> Trust you are doing well. I am doing good, I started my PhD at the LMB under
> Madan Babu and I am six months into it.
> I recently came across your paper titled "Residue contact-count potentials
> are as effective as residue-residue contact-type potentials for ranking
> protein decoys" and it was a very interesting read. On a related note, I
> would like to ask you for some advice.
> I would like to compare the non covalent interaction energy between a given
> pair of residues in different conformational states of a protein. I was
> wondering if there is a software/program using which I could use to compute
> residue-residue interaction potential given a protein structure.
> Best,
> AJ
> --
> --------------------------------------------
> A.J.Venkatakrishnan
> Ph.D. Student
> St. Johns College
> MRC Lab of Molecular Biology
> University of Cambridge
> --------------------------------------------
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